Images cliquables
Clicking on the html file (generated by biojs)
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Warning: use the horizontal scrollbar of the window + the right click of the mouse on the alignment to see the left part of the representation.
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To change the aligments colors (“Nucleotide” recommanded for nucleotides):
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To annotate the FR and CDR regions, use the biojs.gff file in the same folder than the opened .html file:
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Schematic illustration of these regions:
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Export as picture does not work well as part of the sequence not displayed are not exported (screenshot). Use Jalview, as explained below.
Jalview
In
Jalview:
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Drag and drop the .fasta file with the same name as the .html file (in the alignment folder), or use the menu file:
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To stain nuc or aa letters:
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Add colors:
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Set a threshold to see the differences:
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A high threshold set all the columns with at least one difference in white:
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A low threshold set all the different minority events in each column in white:
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To add features:
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Drag and drop a jalview.gff file on the sequence, or use the menu file:
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To change the feature colors:
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To reset the features:
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To export as .png for instance:
Abalign
In Abalign, import a fasta file from the alignment folder and analyze interactively.
Warning: if the align_seq parameter of the nextflow.config file is query, then the vizualization is performed only for the aa sequences that are in phase (i.e., that have identifiable v, d or j regions).